Hi amber community,
I am learning how to do thermodynamic integration using amber8. I would
like to mutate Alanine to Glycine by mutating the side chain CH3 to H.
Here is what I did in tleap. Please let me know what I am doing wrong.
Thank you
a = sequence{ALA}
set a pert true
set a.CB pertName HA3
set a.CB pertType H1
set a.CB pertCharge 0.000
set a.HB1 pertName DUMM
set a.HB1 pertType DU
set a.HB1 pertCharge 0.000
set a.HB2 pertName DUMM
set a.HB2 pertType DU
set a.HB2 pertCharge 0.000
set a.HB3 pertName DUMM
set a.HB3 pertType DU
set a.HB3 pertCharge 0.000
saveAmberParmPert a ala_p.parm ala_p.rst
And the leap.log file produced the following message.
> set a.CB pertCharge 0.000
a.CB: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
>
> set a.HB1 pertName DUMM
a.HB1: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set a.HB1 pertType DU
a.HB1: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set a.HB1 pertCharge 0.000
a.HB1: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
>
> set a.HB2 pertName DUMM
a.HB2: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set a.HB2 pertType DU
a.HB2: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set a.HB2 pertCharge 0.000
a.HB2: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
>
> set a.HB3 pertName DUMM
a.HB3: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set a.HB3 pertType DU
a.HB3: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set a.HB3 pertCharge 0.000
a.HB3: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
>
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Received on Wed Jul 26 2006 - 06:07:14 PDT
